How to study biofilms: technological advancements in clinical biofilm research

Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.

Oral Microcosm Biofilms Grown under Conditions Progressing from Peri-Implant Health, Peri-Implant Mucositis, and Peri-Implantitis

Peri-implantitis is a disease influenced by dysbiotic microbial communities that play a role in the short- and long-term outcomes of its clinical treatment. The ecological triggers that establish the progression from peri-implant mucositis to peri-implantitis remain unknown. This investigation describes the development of a novel in vitro microcosm biofilm model. Biofilms were grown over 30 days over machined titanium discs in a constant depth film fermentor (CDFF), which was inoculated (I) with pooled human saliva. Following longitudinal biofilm sampling across peri-implant health (PH), peri-implant mucositis (PM), and peri-implantitis (PI) conditions, the characterisation of the biofilms was performed. The biofilm analyses included imaging by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), selective and non-selective culture media of viable biofilms, and 16S rRNA gene amplification and sequencing. Bacterial qualitative shifts were observed by CLSM and SEM across conditions, which were defined by characteristic phenotypes. A total of 9 phyla, 83 genera, and 156 species were identified throughout the experiment. The phyla Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria showed the highest prevalence in PI conditions. This novel in vitro microcosm model provides a high-throughput alternative for growing microcosm biofilms resembling an in vitro progression from PH-PM-PI conditions.

In vitro model systems for exploring oral biofilms: From single-species populations to complex multi-species communities

Numerous in vitro biofilm model systems are available to study oral biofilms. Over the past several decades, increased understanding of oral biology and advances in technology have facilitated more accurate simulation of intraoral conditions and have allowed for the increased generalizability of in vitro oral biofilm studies. The integration of contemporary systems with confocal microscopy and 16S rRNA community profiling has enhanced the capabilities of in vitro biofilm model systems to quantify biofilm architecture and analyse microbial community composition. In this review, we describe several model systems relevant to modern in vitro oral biofilm studies: the constant depth film fermenter, Sorbarod perfusion system, drip-flow reactor, modified Robbins device, flowcells and microfluidic systems. We highlight how combining these systems with confocal microscopy and community composition analysis tools aids exploration of oral biofilm development under different conditions and in response to antimicrobial/anti-biofilm agents. The review closes with a discussion of future directions for the field of in vitro oral biofilm imaging and analysis.

Quantifying the demineralisation of enamel using a hyperspectral camera measuring fluorescence loss

BACKGROUND

The gold standard for quantifying mineral loss of enamel is transverse microradiography (TMR) and is complimented by the non-destructive quantitative light induced fluorescence (QLF) which measures changes in autofluorescence. Fluorescence loss has been shown to correlate with mineral loss. Building upon the established method, the use of hyperspectral fluorescence imaging (HI) allows the capture of a broader range of wavelengths to quantify fluorescence changes more accurately.

METHODS

Bovine Enamel was demineralised within the dual constant depth film fermenter over 14 days and analysed using TMR, QLF and HI. The mineral change values were compared using Pearson's Correlation Coefficient.

RESULTS

The analysis showed a statistically significant correlation that was equal between TMR and HI (r = 0.844) and TMR and QLF (r = 0.844), but weaker between QLF and HI (r = 0.811).

CONCLUSIONS

The correlations indicate that HI is a promising valid non-destructive method for quantifying mineral loss from bovine enamel that is as accurate as QLF and complements TMR.

The cariogenic effect of starch on oral microcosm grown within the dual constant depth film fermenter

Evidence on the link between starch intake and caries incidence is conflicting, therefore the cariogenicity of starch compared with sucrose was explored using a dual Constant Depth Film Fermenter (dCDFF) biotic model system. Bovine enamel discs were used as a substrate and the dCDFF was inoculated using human saliva. CDFF units were supplemented with artificial saliva growth media at a constant rate to mimic resting salivary flow rate over 14 days. The CDFF units were exposed to different conditions, 2% sucrose or 2% starch 8 times daily and either no additional fluoride or 1450 ppm F- twice daily. Bovine enamel discs were removed at intervals (days 3, 7, 10 and 14) for bacterial enumeration and enamel analysis using Quantitative Light Induced Fluorescence (QLF) and Transverse Microradiography (TMR). Results showed that in the absence of fluoride there was generally no difference in mineral loss between enamel exposed to either sucrose or starch when analysed using TMR and QLF (P > 0.05). In the presence of fluoride by day 14 there was significantly more mineral loss under starch than sucrose when analysed with TMR (P < 0.05). It was confirmed that starch and sucrose are similarly cariogenic within the dCDFF in the absence of fluoride. With the aid of salivary amylase, the bacteria utilise starch to produce an acidic environment similar to that of bacteria exposed to sucrose only. In the presence of fluoride, starch was more cariogenic which may be due to the bacteria producing a more hydrophobic intercellular matrix lowering the penetration of fluoride through the biofilm. This is significant as it indicates that the focus on sugars being the primary cause of caries may need re-evaluating and an increase in focus on carbohydrates is needed as they may be similarly cariogenic as sugars if not more so.

Evaluation of ion release and the recharge ability of glass-ionomer cement containing BioUnion filler using an in vitro saliva-drop setting assembly

OBJECTIVE

A glass-ionomer cement (GIC) containing BioUnion filler has been reported to release Zn²⁺ under acidic conditions and to inhibit oral bacteria on its surface. However, previous results are based on in vitro experiments under static conditions. This study aimed to assemble an in vitro saliva-drop setting to simulate in vivo conditions of the oral cavity and to investigate the ion releasing and recharging properties of the GIC containing BioUnion filler.

METHODS

The effective concentrations of Zn²⁺ and F^- against Streptococcus mutans and saliva-derived multi-species biofilms were determined. Artificial saliva was dropped on the GIC containing BioUnion filler using the in vitro saliva-drop setting assembly and was periodically replaced with acetic acid. Ion release/recharge properties were investigated by measuring the release concentrations of Zn²⁺ and F^-.

RESULTS

The concentration of Zn²⁺ released from the BioUnion filler-containing GIC during seven days with repeated exposure to acid could be maintained at the level to inhibit S. mutans and saliva-derived multi-species biofilm formation. Moreover, the BioUnion filler-containing GIC could be recharged with Zn²⁺ and F^- by the application of a tooth gel containing Zn²⁺ and F^-. The release concentration of Zn²⁺ after recharging was significantly higher than the effective concentration of Zn²⁺ to hinder S. mutans and saliva-derived multi-species biofilm formation on material surfaces.

SIGNIFICANCE

The GIC containing BioUnion filler was shown to have the potential to inhibit biofilm formation in the oral cavity. In addition, recharging Zn²⁺ and F^- would further enhance the effect of the GIC containing BioUnion filler.

A Multispecies Biofilm In Vitro Screening Model of Dental Caries for High-Throughput Susceptibility Testing

There is a current need to develop and optimize new therapeutics for the treatment of dental caries, but these efforts are limited by the relatively low throughput of relevant in vitro models. The aim of this work was to bridge the 96-well microtiter plate system with a relevant multispecies dental caries model that could be reproducibly grown to allow for the high-throughput screening of anti-biofilm therapies. Various media and inoculum concentrations were assessed using metabolic activity, biomass, viability, and acidity assays to determine the optimal laboratory-controlled conditions for a multispecies biofilm composed of Streptococcus gordonii, Streptococcus mutans, and Candida albicans. The selected model encompasses several of the known fundamental characteristics of dental caries-associated biofilms. The 1:1 RPMI:TSBYE 0.6% media supported the viability and biomass production of mono- and multispecies biofilms best. Kinetic studies over 48 h in 1:1 RPMI:TSBYE 0.6% demonstrated a stable biofilm phase between 10 and 48 h for all mono- and multispecies biofilms. The 1:1:0.1 S. gordonii: S. mutans: C. albicans multispecies biofilm in 1:1 RPMI:TSBYE 0.6% is an excellent choice for a high-throughput multispecies model of dental caries. This high-throughput multispecies model can be used for screening novel therapies and for better understanding the treatment effects on biofilm interactions and stability.

Arginine Exposure Decreases Acidogenesis in Long-Term Oral Biofilm Microcosms

Arginine is used in dental health formulations to help prevent dental cavities. This study assessed the effects of the long-term dosing of laboratory dental plaques with an arginine dentifrice. Data indicate that the addition of arginine dentifrice during sucrose challenge significantly increased plaque pH, thus potentially mitigating cariogenesis. Several functional groups of bacteria associated with tooth decay were significantly decreased in the laboratory plaques during exposure to the arginine dentifrice.

Arginine is an important pH-elevating agent in the oral cavity. It has been incorporated in oral hygiene formulations to mitigate sensitivity and to prevent caries. In this investigation, the effects of sustained arginine dosing of dental plaque microcosms on bacteriological composition and pH were evaluated under controlled conditions. Plaque microcosms were established in constant-depth film fermentors (CDFFs) using salivary inocula and fed continuously with artificial saliva. To simulate resting and cariogenic states, the CDFFs were supplemented with sterile water or 5% sucrose, respectively. Plaques were then dosed twice daily with a dentifrice with 1.5% arginine arginine added (DA) or without arginine (DN). This regimen continued for over 3 weeks, after which fermentors were maintained without dosing. Microcosms were analyzed by differential viable counting, with a pH microelectrode, and by eubacterial DNA profiling. Sucrose dosing was associated with significantly (P < 0.001) decreased pH, significantly (P < 0.05) increased counts of total aerobes, Gram-negative anaerobes, aciduric species, acidogenic species, arginine utilizing species, bifidobacteria, lactobacilli and streptococci, and significant (P < 0.05) changes in DNA profiles. Plaques dosed with DA had a significantly (P < 0.001) higher pH than those dosed with DN, with or without sucrose supplementation. Dosing with DA but not DN significantly (P < 0.05) decreased counts of all functional bacterial groups apart from the total anaerobes in cariogenic plaques, and in resting plaques, dosing with DA significantly (P < 0.05) decreased counts of streptococci, lactobacilli, bifidobacteria, and acidogenic bacteria. In summary, sustained exposure of oral microcosms to arginine in formulation significantly increased plaque pH and significantly reduced the viability of cariogenic bacterial species.

IMPORTANCE Arginine is used in dental health formulations to help prevent dental cavities. This study assessed the effects of the long-term dosing of laboratory dental plaques with an arginine dentifrice. Data indicate that the addition of arginine dentifrice during sucrose challenge significantly increased plaque pH, thus potentially mitigating cariogenesis. Counts of several functional groups of bacteria associated with tooth decay were significantly decreased in the laboratory plaques during exposure to the arginine dentifrice.

Evidence of an in vitro Coupled Diffusion Mechanism of Lesion Formation within Microcosm Dental Plaque

The purpose of this study was to determine whether or not the dual constant-depth film fermenter (dCDFF) is able to produce caries-like enamel lesions and to ascertain further information regarding the performance of this fully functional biological caries model. Conditions were defined by the continuation (CF) or cessation (FF) of a saliva-type growth medium supply during 50-mM sucrose exposures (8 times daily). Hydroxyapatite (n = 3) and bovine enamel (n = 3) substrata were included within each condition and samples extracted after 2, 4, 8, and 16 days. Community profiles were generated for fastidious anaerobes, Lactobacillus spp., Streptococcus spp., mutans streptococci (MS), and Veillonella spp. using selective culture techniques and enamel demineralisation assessed by transverse microradiography. Results demonstrated that the dCDFF model is able to produce caries-like enamel lesions with a high degree of sensitivity where reduced ionic strength within the FF condition increased surface layer mineral deposition. Between conditions, biofilm communities did not differ significantly, although MS in the biofilms extracted from the FF condition rose to a higher proportion (by 1.5 log10 units), and Veillonella spp. were initially greater within the CF condition (by 2.5 log10 units), indicating an enhanced ability for the clearance of low-pKa acids following exposures to sucrose. However, both conditions retained the ability for caries-like lesion formation.

Reproducible biofilm cultivation of chemostat-grown Escherichia coli and investigation of bacterial adhesion on biomaterials using a non-constant-depth film fermenter

Biomaterials-associated infections are primarily initiated by the adhesion of microorganisms on the biomaterial surfaces and subsequent biofilm formation. Understanding the fundamental microbial adhesion mechanisms and biofilm development is crucial for developing strategies to prevent such infections. Suitable in vitro systems for biofilm cultivation and bacterial adhesion at controllable, constant and reproducible conditions are indispensable. This study aimed (i) to modify the previously described constant-depth film fermenter for the reproducible cultivation of biofilms at non-depth-restricted, constant and low shear conditions and (ii) to use this system to elucidate bacterial adhesion kinetics on different biomaterials, focusing on biomaterials surface nanoroughness and hydrophobicity. Chemostat-grown Escherichia coli were used for biofilm cultivation on titanium oxide and investigating bacterial adhesion over time on titanium oxide, poly(styrene), poly(tetrafluoroethylene) and glass. Using chemostat-grown microbial cells (single-species continuous culture) minimized variations between the biofilms cultivated during different experimental runs. Bacterial adhesion on biomaterials comprised an initial lag-phase I followed by a fast adhesion phase II and a phase of saturation III. With increasing biomaterials surface nanoroughness and increasing hydrophobicity, adhesion rates increased during phases I and II. The influence of materials surface hydrophobicity seemed to exceed that of nanoroughness during the lag-phase I, whereas it was vice versa during adhesion phase II. This study introduces the non-constant-depth film fermenter in combination with a chemostat culture to allow for a controlled approach to reproducibly cultivate biofilms and to investigate bacterial adhesion kinetics at constant and low shear conditions. The findings will support developing and adequate testing of biomaterials surface modifications eventually preventing biomaterial-associated infections.

Continuous culture of sessile human oropharyngeal microbiotas

The microbiota of the human oropharynx plays an important role in health through involvement in the aetiology of infection and the carriage of adventitious pathogens. Despite this, there are few models available for the preclinical assessment of novel antimicrobials directed to the human throat. We have profiled bacterial consortia sampled from the palatine tonsil and posterior pharyngeal wall microbiotas of healthy adult volunteers (n = 10) using differential culture and 16S rRNA gene sequencing, together with PCR-denaturing gradient gel electrophoresis. The data generated were used to assess the validity of an oropharyngeal microcosm system based on replicated constant-depth film fermenters (CDFFs; n = 5), which were continuously fed using an artificial airway surface liquid. Developed microcosms exhibited significant homology to ex situ consortia according to principal components analysis, whilst compositional reproducibility was apparent in replicated models for tonsillar and pharyngeal inocula. Differential viable count data and Shannon-Weiner diversity indices indicated that representative tonsil and pharyngeal model systems achieved dynamic compositional stability about 6 days after inoculation which could be maintained for ≥20 days. In conclusion, the CDFF facilitated the continuous maintenance of bacteriologically stable microcosms that were compositionally similar to ex situ inocula.